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- PDB-3sb4: Crystal structure of a leucine-rich repeat protein (BT_1240) from... -

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Basic information

Entry
Database: PDB / ID: 3sb4
TitleCrystal structure of a leucine-rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution
ComponentsHypothetical leucine rich repeat protein
KeywordsPROTEIN BINDING / LRR / RIGHT-HANDED BETA-ALPHA SUPERHELIX / LEUCINE-RICH REPEAT / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology: / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta / Leucine-rich repeat domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical leucine rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Structure summary
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical leucine rich repeat protein
B: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,30616
Polymers73,9152
Non-polymers1,39114
Water7,512417
1
A: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,78610
Polymers36,9571
Non-polymers8299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5206
Polymers36,9571
Non-polymers5635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.210, 62.130, 66.860
Angle α, β, γ (deg.)109.800, 93.750, 91.050
Int Tables number1
Space group name H-MP1
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Hypothetical leucine rich repeat protein


Mass: 36957.336 Da / Num. of mol.: 2 / Fragment: sequence database residues 22-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1240 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A8C7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 22-349 OF THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.31 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.00% Glycerol, 0.0400M KH2PO4, 16.00% PEG-8000, No Buffer, pH None, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97999,0.97959
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 22, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979991
30.979591
ReflectionResolution: 1.99→27.817 Å / Num. obs: 52132 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.98 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 5.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.2782.590447876172.7
2.07-2.150.2193.2112879779192
2.15-2.250.1823.71197810418192.2
2.25-2.370.1274.31183210324193.1
2.37-2.520.1124.81190110447193.7
2.52-2.710.0935.41140610076194.4
2.71-2.990.08861210510759195.2
2.99-3.420.0786.61151110339195.2
3.42-4.30.0771159910490195.7
4.3-27.8170.0727.11119910192192.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.99→27.817 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9362 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) AND PEG (PG4) FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. 4. THE REFINEMENT WAS RESTRAINED AGAINST MAD PHASES. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 2653 5.1 %RANDOM
Rwork0.168 ---
obs0.1696 52044 --
Displacement parametersBiso max: 116.72 Å2 / Biso mean: 48.9168 Å2 / Biso min: 22.95 Å2
Baniso -1Baniso -2Baniso -3
1-4.2862 Å25.6707 Å2-2.6392 Å2
2--1.6167 Å2-8.6283 Å2
3----5.9029 Å2
Refinement stepCycle: LAST / Resolution: 1.99→27.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 91 417 5618
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2568SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes779HARMONIC5
X-RAY DIFFRACTIONt_it5420HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion725SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6931SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5420HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7314HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion2.73
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2198 159 4.37 %
Rwork0.1777 3476 -
all0.1795 3635 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75270.572-0.76842.3397-0.59991.8827-0.08240.0554-0.077-0.1944-0.0009-0.08750.18750.01990.0833-0.0206-0.0393-0.0106-0.023-0.0052-0.143525.4759-7.959221.4514
21.44050.2741-0.06881.2987-0.0292.5985-0.07620.17640.0612-0.10460.01350.0733-0.1166-0.15920.0627-0.1095-0.010.0105-0.09170.00430.03398.94660.351346.7279
32.09751.1105-0.01972.2723-0.44981.355-0.15160.181-0.0173-0.22280.0990.02170.1139-0.0120.0526-0.0176-0.00070.0367-0.0955-0.0287-0.060429.7218-34.046343.2766
41.4282-0.3347-0.09022.07380.19841.3035-0.0178-0.1172-0.08450.20060.0168-0.14290.08360.03790.001-0.0763-0.0180.0051-0.03390.0275-0.033242.2721-14.301962.9648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - A|196}A0 - 196
2X-RAY DIFFRACTION2{A|197 - A|349}A197 - 349
3X-RAY DIFFRACTION3{B|22 - B|196}B22 - 196
4X-RAY DIFFRACTION4{B|197 - B|349}B197 - 349

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